Someone with the moniker DrREC replied to my posting about the complexity of the last eukaryotic ancestor as follows:
This is almost a tautology. The last Eukaryotic common ancestor had the defining features of a Eukaryote….which happen to be more complex than prokaryotic life.
There is no tautology at work here. Not even close. We can appreciate this by simply recognizing that scientists could very well have discovered that LECA was remarkably simple. For example, it could have been a cell with a nucleus, but lacking protein-coding introns, mitochondria, golgi bodies, ubiquitin, and flagella. And its nuclear pore complex, cytoskeleton, and endomembranous system could have been rather simple. But as it turned out, LECA had a level of complexity that rivals modern day cells.
Of course, we don’t need to be hypothetical about this. Back in the 1980s, biologists expected LECA to have been rather simple. Consider the simplest of eukaryotic cells – microsporidia.
Microsporidia are intracellular parasites that infect most other eukaryotic cells, although arthropods are the most commonly parasitized. They are the simplest and smallest eukaryotic cells and thus represent a textbook example of reductive evolution [1]. Here’s a figure that shows how “bacterial” they look like:
Whereas scientists once classified microsporidia as protozoa, it is now generally recognized that they are highly evolved fungi.
In the 1980s, scientists viewed microsporidia as the most primitive example of a eukaryote. How is it they mistakenly viewed a highly evolved fungus for a primitive protozoan? In their review [2], Patrick J. Keeling and Naomi M. Fast explain the situation as follows:
However, in 1983, attention was drawn to the possible evolutionary significance of microsporidia in a new way. Cavalier-Smith proposed that the origin of eukaryotes might have preceded the endosymbiotic origin of the mitochondrion by some considerable span of time, implying that there may be protists that evolved before the mitochondrial origin. In other words, there may be primitively amitochondriate eukaryotes, and focusing attention on these protists could unlock some of the secrets surrounding the origin of eukaryotes. Four lineages of amitochondriate protists that could hold this pivotal position were identified, and these were collectively named Archezoa: Archamoebae (e.g., Entamoeba), Metamonada (e.g., Giardia), Parabasalia (e.g., Trichomonas), and Microsporidia.
Lev Seravin, from the Biological Research Institute of St. Petersburg State University, recounts how Cavalier-Smith has to quickly dismantle Archezoa soon after establishing it [3]. He explains why Cavalier-Smith introduced this classification scheme:
Proceeding from a fairly widely spread point of view that the simpler the living organisms the more originally primitive they should be, he united the macrotaxa including the flagellates and amoeboid organisms devoid of mitochondria into a single subkingdom Archezoa as a phylogenetically initial state for all the rest of the Protozoa kingdom.
Clearly, Cavalier-Smith was misled by the assumption that “simple = primitive.” Nevertheless, and here is the key point, there was a very impressive list of evidence that supported Cavalier-Smith’s classification.
I already mentioned that microsporidia are the smallest and simplest eukaryote. They not only lack mitochondria, but also lack other widely distributed eukaryotic organelles such as flagella, golgi bodies, and peroxisomes. So it would appear that microsporidia branched off the eukaryotic tree prior to the emergence of these organelles. This hypothesis was supported by more scientific discoveries
1. Their genomes can be smaller than those of bacteria. For example, one species of microsporidia has a genome with 2.3 million nucleotides, while E. coli‘s genome is around 4.6 million nucleotides [1].
2. What was even more remarkable was the bacterial-like ribosome of microsporidia. The eukaryotic ribosome is known as the 80S ribosome (a rough measure of its size), while bacteria possess 70S ribosomes. Microsporidia have 70S ribosomes, meaning that their ribosomes are about the same size as those found in bacteria. And what’s even more striking is that their 5.8S rRNA and 28S rRNA are fused. This is what we see in bacteria. This fusion occurs at the level of the rRNA genes, again as in bacteria.
3. Then the case got even stronger:
Shortly after the Archezoa hypothesis was formulated, the tools of molecular phylogenetics began to be applied vigorously to microbial eukaryotes, and the first molecular data from microsporidia lent extraordinary support to the Archezoa hypothesis. The small subunit ribosomal RNA (SSU rRNA) from the microsporidian Vairimorpha was shown to be the earliest branch on the eukaryotic tree, and of greater interest, the microsporidia were found to be the only eukaryotes to retain the prokaryotic trait of having their 5.8S rRNA fused to the large subunit (LSU) rRNA. These two pieces of evidence bolstered the notion that microsporidia were indeed an ancient and primitive lineage, and further evidence seemed to accumulate with the sequencing of every new microsporidian gene: Phylogenies based on elongation factor 1alpha, elongation factor 2, as well as isoleucyl tRNA synthetase, all showed the microsporidia branching deeply.
The same apparent early phylogenetic position was also seen with other Archezoa (with the possible exception of Entamoeba), and altogether the case of an ancient origin and primitive lack of mitochondria for microsporidia and other Archezoa seemed neatly sewn up. [2]
Yet it was all wrong. A closer analysis of the microsporidian genome found evidence of many mitochondrial genes. And a closer look at genes for tubulin, elongation factors, heat shock proteins, and the RNA polymerase, found that microsporidia clustered with fungi. As of today, most scientists (including Cavalier-Smith) reject the existence of Archezoa and recognize microsporidia as highly derived parasitic fungi.
1. Andersson SG, Kurland CG. 1998. Reductive evolution of resident genomes. Trends Microbiol6:263-8.
2. Keeling, PJ and Fast, NM. 2002. MICROSPORIDIA: Biology and Evolution of Highly Reduced Intracellular Parasites. Annu. Rev. Microbiol. 56:93-116.
designmatrix.wordpress.com 
Pingback: Complexity of earliest animal/plant cell is real. “No tautology at work here.” | Uncommon Descent
For some odd reason, DrREC does not want to reply here. But here is his reply from the pingback above:
DrREC
07/16/2011
9:22 pm
Oh goodness, this is bad.
Mike Gene, do you recognize the difference between FIRST and LAST?
L as in LUCA or LECA is LAST-The Last Eukaryotic Common Ancestor, the most RECENT (not oldest) organism from which all organisms/all Eukaryotic organisms (respectively) living on Earth descend.
Not the First! Do you understand LECA isn’t the first Eukaryote?
So “it could have been a cell with a nucleus, but lacking protein-coding introns, mitochondria, golgi bodies, ubiquitin, and flagella” is an argument that might apply to “FECA” the first common Eukaryote–which we can’t reasonably infer the details of–but not LECA!
Arguing LECA was simple and lacking all those things leads to the poor hypothesis that introns, spliceosomes, mitochondria, golgi, ubiquitin and flagella evolved multiple independent times in Eukarya-in a homologous manner, having the same features and detectable sequence homology in each lineage!
Simply put, if it isn’t in the LAST Eukaryotic Common ancestor, Eukarya must have invented those things multiple times, in the same way, which is way unlikel.
But you’re still going on and on about a ‘simple’ Eukaryote lacking those things. Entirely possible. Probable, even. Relevant to LECA? No!
Microsporidia are considered fungi that lost many Eukaryotic features in becoming more efficient parasites. Your consideration of them is interesting in terms of basal/primitive Eukarya, but not LECA. You even say they “thus represent a textbook example of reductive evolution.”
So how the hell do they represent a common ancestor, having later lost these key features? Maybe they might impact our view of a simple, primordial Eukaryote, but LECA that ain’t.
Do you think LUCA was the first life?
My my…..
Perhaps this is why the second part of my reply, that “Curious also to invoke LECA, which assumes common ancestry of all Eukarya. This is a technique of using modern sequences to peer back and infer what was.
Using this assumes there are not multiple origins of Eukarya, and could even be interpreted as ruling out design, as those lines of descent are unbroken and unperturbed (otherwise, we can’t infer what was in LECA-a more modern insertion of a common design kind of rules out inferring what was commonly present in an ancient organism). I grant this isn’t mutually exclusive with some versions of ID, but it nearly reduces it to theistic evolution.”
Is more interesting. If you understood what you were invoking in support of ID, then where do you stand?
DrREC’s reply is rooted in some serious confusion. First, nowhere did I claim that LECA was the first eukaryote. So when he write, “Not the First! Do you understand LECA isn’t the first Eukaryote?”, he is only shadow boxing.
Second, he doesn’t seem to grasp the significance of the abandoned Archezoa classification. He must have skimmed over the observations of Keeling and Fast:
If it turned out that microsporidia were primitive protozoans, it would not mean that “mitochondria…..evolved multiple independent times in Eukarya-in a homologous manner, having the same features and detectable sequence homology in each lineage!” It would simply mean that microspordia represent a lineage that split off the branch that later acquired mitochondria. That was precisely the hypothesis behind the Archezoa classification.
And guess what? This same logic would apply to flagella, golgi bodies, etc.
DrRec:
So “it could have been a cell with a nucleus, but lacking protein-coding introns, mitochondria, golgi bodies, ubiquitin, and flagella” is an argument that might apply to “FECA” the first common Eukaryote–which we can’t reasonably infer the details of–but not LECA!
Wrong. There are extant protists that do lack protein-coding introns, mitochondria, golgi, and flagella. If these extant protists turned out to be basal rather than derived, not only would this validate the Archezoa classification, it would entail a simple LECA.
Microsporidia are considered fungi that lost many Eukaryotic features in becoming more efficient parasites.
But that’s not how C-S originally classified them, now is it?
Your consideration of them is interesting in terms of basal/primitive Eukarya, but not LECA.
I just explained why this is wrong. Let me add something more from Poole and Penny:
In the mid-1990s, a somewhat pedestrian view of eukaryotic origins, the ‘archezoa hypothesis’, held sway. This maintained that a protoeukaryote (with nucleus) engulfed the mitochondrial ancestor. Supporting the theory were ‘archezoa’, anaerobic eukaryotes with no mitochondria. Archezoa apparently populated the oldest branches of the eukaryote tree, suggesting that eukaryotes began diversifying before mitochondria entered the picture.
The archezoa hypothesis is thus composed of two independent hypotheses: (a) that a protoeukaryote host (PEH) engulfed the mitochondrial ancestor, and (b) that modern archezoa are ‘missing links’ that never possessed mitochondria. Hypothesis (b) is now unanimously rejected: every archezoan examined bears vestigial mitochondria, or genes inherited from mitochondria. Thus, all modern eukaryotes evolved from a mitochondrionbearing ancestor
If LECA was roughly as complex as extant eukaryotes, there would be no basis for thinking of the ‘archezoa’ as ‘missing links.’ They were considered ‘missing links’ because they were supposed to link a simple LECA to a complex extant eukaryotic state.
Perhaps this is why the second part of my reply….Is more interesting. If you understood what you were invoking in support of ID, then where do you stand?
I already replied to that.
The analysis and conclusions regarding LECA and the organisms discussed in the article depend upon evolutionary assumptions to interpret the science – regardless. So, there’s an argument that the position represented is a tautology, and possiblly that the whole argument is a form of “Begging the question.”
(Could have been if the Darwinian mechanism applies, which it may in the case “reductive evolution”, but doesn’t necessarily apply to a “common ancestor, and if there was a LECA. That would be hard to ascertain, conclusively, on sciencific grounds, without applying some amount of question begging concerning unproven assumptions which are part of the article’s contention from the get-go.)